Social behavior can alter microbiome composition via transmission among social partners. Common marmosets (Callithrix jacchus) live in socially monogamous pairs, and social behavior between pairmates is characterized by high rates of grooming, sniffing, and proximity. Males exhibit more grooming, sniffing, and sociosexual behavior than females at the onset pairing. We collected fecal samples on 8 unrelated male-female pairs prior to pairing (PRE), and for 8 weeks after pairing (POST), and sequenced 16S Ribosomal RNA to characterize the gut microbiome in the two phases of the study. Marmoset pairs had a higher number of shared gut microbial groups and similarity of gut microbial communities in the POST phase, relative to PRE (Unweighted UniFrac distance: paired t-test, p < 0.05). Male fecal samples harbored more female-origin gut microbes after pairing, especially early in pairing (Mann-Whitney test, p < 0.05), which may be linked to sex bias in the frequencies of social behavior. There were significant increases and transmission of succinate producing (Anaerobiospirillum) and succinate-utilizing and propionic acid producing bacteria (Phascolarctobacterium) in POST along with a corresponding decline of dominant taxa such as Bifidobacterium. The invasion also resulted in significantly increased short-chain fatty acid (SCFA) concentrations in the fecal material. The synchronized gut microbiome of the common marmoset during social bond establishment may contribute to physiological homeostasis in the early stage of pair-bond formation. The putative changes in gut microbiomes in marmosets during pair-bond formation is a potential model to investigate the correlation between social behavior and gut microbial transmission and ecological characteristics.